I did do the full pan removal on my e39 a couple of years ago. It had the expected amount of metallic reside at the bottom of the pan, and cut up the filter to have a look inside but it did not have anything in it. What was the condition of your transmission when you had the pan out?
I used the same Esso LT fluid as what BMW specifies for the ZF gearbox. Gearbox still feels very strong today and the car has 240,000 kms on the odometer which is roughly 150,000 miles. If I were to do another service to the gearbox again, I will just change the fluid and wouldn't bother with opening up the pan.